PayPal has confirmed to us the warnings that appear on login to their site are due to issues they'd logged going back prior to June 5th, and that they are not seeing any issues logged since June 6th for any merchant we've asked them to check. The fact that you are still processing payments successfully now, after their cutoff deadline, confirms that things are set up and working as they require.
BTW, when you use E-junkie it's not necessary to upgrade your site to use HTTPS or TLS 1.2, as your own server is not interfacing with PayPal's system at all, nor is your site handling any payment data subject to PCI-DSS compliance requirements; we handle all of that for you at our end.